SAXSdb — 1h1o

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1h1o
沉积日期 deposition_date	2002-07-19
结构标题 title	Acidithiobacillus ferrooxidans cytochrome c4 structure supports a complex-induced tuning of electron transfer
关键词 keywords	ELECTRON TRANSPORT, C4, CYTOCHROME, ELECTRON TRANSFER, HEME; ELECTRON TRANSPORT
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	22.04 Å
回转半径 Rg (电子) rg_electron	21.58 Å
零角强度 I(0) i0	29777300.00
分子量 molecular_weight	40549.0 kDa
排除体积 excluded_volume	49908 Å³
包络体积 envelope_volume	55244 Å³
水化壳体积 shell_volume	21525 Å³
包络直径 envelope_diameter	72.6 Å
壳层 Rg shell_rg	27.94 Å
包络 Rg envelope_rg	21.81 Å
形状 Rg shape_rg	21.56 Å
总 Rg total_rg	22.39 Å
总原子数 total_atoms	2812
残基数 n_residues	342
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	71.6 Å
Rg (实空间) rg_real	22.04 Å
Rg 误差 (实空间) rg_real_error	0.40 Å
I(0) (实空间) i0_real	2.9780e+07
I(0) 误差 (实空间) i0_real_error	3.6010e+05
Rg (倒空间) rg_reciprocal	22.04 Å
I(0) (倒空间) i0_reciprocal	29780000.0000
解质量估计 total_estimate	0.6982
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	23.5 Å
偏度 Skewness skewness	0.311
峰度 Kurtosis kurtosis	-0.501
角度范围 angular_range	— – 0.3600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6437000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.967; Smooth: 0.994

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	CYTOCHROME C-552
分子量 formula_weight	19936.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	2998

VGSADAPAPYRVSSDCMVCHGMTGRDTLYPIVPRLAGQHKSYMEAQLKAYKDHSRADQNGEIYMWPVAQALDSAKITALADYFNAQKPPMQSSGIKHAGAKEGKAIFNQGVTNEQIPACMECHGSDGQGAGPFPRLAGQRYGYIIQQLTYFHNGTRVNTLMNQIAKNITVAQMKDVAAYLSSL

Entity 2 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	186

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1h1oa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.4 — Two-domain cytochrome c

结构域编号 domain_id	d1h1oa2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.4 — Two-domain cytochrome c

结构域编号 domain_id	d1h1ob1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.4 — Two-domain cytochrome c

结构域编号 domain_id	d1h1ob2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.3 — Cytochrome c
超家族 Superfamily superfamily	a.3.1 — Cytochrome c
家族 Family family	a.3.1.4 — Two-domain cytochrome c

CATH v4.4 (4 domains)

结构域编号 domain_id	1h1oA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

结构域编号 domain_id	1h1oA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

结构域编号 domain_id	1h1oB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

结构域编号 domain_id	1h1oB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cytochrome c-like domain

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7. 引用文献 (1)

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晶胞边长 a length_a	100.049 Å
晶胞边长 b length_b	100.049 Å
晶胞边长 c length_c	149.668 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 64 2 2
空间群编号 int_tables_number	181
晶系 crystal_system	—

分辨率 resolution	2.130 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.2840

fit	/app/data/saxs_computation/h1/1h1o/1h1o.fit
pddf	/app/data/pr_computation/h1/1h1o/1h1o.pr.out
profile	/app/data/saxs_computation/h1/1h1o/1h1o.dat

Acidithiobacillus ferrooxidans cytochrome c4 structure supports a complex-induced tuning of electron transfer

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)